I just noticed that I introduced a bug in 0.99.05.037, so I'm rushing out a fix. The bug made the program crash when scanning files that have an empty frame inside ID3V2 tags. True, ID3V2 tags aren't supposed to contain empty frames, but MP3 Diags shouldn't crash because of them either.
Another small change is that now the custom transformation list #4 gets populated by default with all the things that are likely to fix the files, so the processing is more automated than ever. I'd still recommend to use the other 3 buttons, for finer control, but if you have many files and don't particularly care that the second ID3V2 tag will get discarded (well, it was invalid to begin with), it's faster to use a single button.
For the few who want to build the program on Windows, there's a big change: there are no longer Windows-specific sources, and build.bat is gone. The way to build now is to use a GUI application (really an HTML page), from which you can generate project files that Qt Creator or Visual C++ can work with, or you can simply press a button to get the program built. See more details on the download page.
As I'm typing this, none of the Linux binaries have finished building, but hpefully it won't take long before they are available.